FRED

A Framework for T-cell Epitope Detection

FRED is a framework for T-cell epitope detection that offers
consistent, easy, and simultaneous access to well established
prediction methods for MHC binding and antigen processing. FRED can
handle polymorphic proteins and offers analysis tools to combine,
benchmark, or compare different methods. It is implemented in Python in
a modular way and can easily be extended by user defined methods.

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Installation

Installation instructions can be found in the README.txt included with the FRED package. FRED was tested on Linux and MacOS.

The Python code of FRED is platform-independent and does not require a
particular operating system, although it has been developed mostly on
Linux. We have also successfully installed FRED on other Unix-derived
platforms, e.g. MacOS X, and on Windows using cygwin.

Tutorial Documentation

A tutorial how to use FRED and the documentation of the API is available here as pdf. The documentation is also available in an html version in an zip archive.

Examples

Some basic examples for the usage of FRED along with all input data
required are included with the FRED package (FRED/examples).

A short description of the examples included in the FRED package can be found here.

Citation

EpiToolKit

EpiToolKit is a web server that
provides simultaneous access to different MHC binding prediction
methods. EpiToolKit also provides predictions of minor
histocompatibility complex antigens (mHags). EpiToolKit is based on
FRED.